Late Night Visitors
by Wedjatqi
Summary: ALLIANCE FIC - John has a visit from a dangerous late night visitor. AU JT. This is the fic that started my 'Alliance AU' world - a PREQUEL to the other Alliance fics.


**Title: **Late Night Visitors

**Part**: 1/1

**Disclaimers**: I make no profit from this and do not plan to (if only you could get paid for your hobbies!)

**Spoilers**: Set in AU world, equivalent to Season 3.

**Note:**Part of Fic Tag with Gater101 (moving on from the Bugfics now). Sorry it's taken so long, but I've had a bloody awful month, so I'm slowly heading back into the writing side of life again. This fic is set in a new AU reality, don't worry I will explain its structure and history as I go along. I have already written some prequels to this story, but liked the idea of jumping into this AU reality somewhere in the middle. There will be questions from this fic I'm sure, but they will be answered with further fics.

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The flat smooth Ancient floor was warm under John's feet as he stood up from the bed and padded slowly across his dark bedroom. He had forgotten to close the curtains across the balcony doors and light was spilling into the room. Though his bladder was protesting he still altered his sleepy course towards the glass balcony doors.

He felt the subtle sensation of the door mechanism as he neared the doors, telling him that the doors could be opened with only a thought, but he didn't want to let the cool night breeze into his quarters. He peered through the glass down towards the closest pier below. Lights glowed across the pier, testimony to the large numbers of people living there, though there were an extra few more this week. Representatives from the many worlds of the loosely governed Alliance were in the city, and had been assigned living quarters on the east pier alongside the already present large numbers of displaced people from Wraith culled worlds.

John looked down at the glowing lights, wondering why so many people were still awake, but then considered that perhaps those people who had lost their homes and families to Wraith culling preferred to sleep with their lights on. And the Alliance negotiators were probably still up plotting away. John sighed wearily.

He had been assigned to watch over the negotiations, which meant he had to stand up all day long forced to listen to arguing politicians; joy. Despite two years of exemplary service in Atlantis, and with only the occasional clash with authority figures, it seemed that Colonel Sumner still distrusted John. John hadn't really cared about his commanding officer's opinion, but after having personally saved the city on several occasions it still wasn't enough for Sumner. Though, since Colonel Carter had been brought in to be the new city leader things had improved slightly. John had been given his own team to lead, which had clearly annoyed Sumner, which only made it all that more fun for John. Sumner had originally kept John in his team obviously to keep an eye on him, but after almost three years John had proved himself to the Powers That Be, even if Sumner still looked at him like he was something bad that had stuck to Sumner's boot.

John was surprised how much he enjoyed being a team leader, despite the fact that Sumner had assigned Rodney to his team. Sumner had clearly taken the opportunity to eject Rodney from his own team, but then John had always worked as an unofficial buffer between Rodney and the Colonel. John guessed Sumner wasn't prepared to cope with Rodney without John, which was fine as Rodney was the smartest person in the city and clearly the best choice of scientist to take off world.

Only last month they had discovered a new Ancient ship and had saved it from near destruction. Most commanders would have been pleased, but not Sumner it appeared, as John's team had been assigned this new babysitting job. Of course it was a dangerous assignment, and that only made John more suspicious of Sumner's motives. Ford's opinion was that Sumner wouldn't go that far, but John thought differently; for watching over the negotiations was like watching over medieval thugs masquerading as kings and queens; all pleasant and well behaved on the surface, but underneath they were looking for the gaps in your chainmail through which they could plunge a knife.

John caught himself shivering at the thought and turned from the balcony doors and headed to the bathroom. The doors slid shut behind him and the lights flickered on to their lowest setting. Today had been a long day of watching over those thugs. Mr Woolsey had struggled to get anything achieved and John had found himself actually feeling sorry for the guy. The Alliance was made up of a large group of super powers all with different cultures, attitudes and expectations. What bound them together was the creation of a united military force which gave the Wraith a serious run for their money. From what John understood of local history before the Alliance military the local worlds had fought independently against the Wraith, only succeeding in battling off the Wraith after long bloody battles. Then the Alliance military was formed, uniting all their military might together to create a massive space faring battle force that took the battle to the Wraith. It had been a bloody and messy war from John's understanding, but somehow they had held their own against the Wraith. Of course their victories only pushed the Wraith into culling non Alliance worlds more, which had lead to such large numbers of displaced people seeking somewhere to live. Of course it had also resulted in many worlds joining the Alliance, only adding to their might and reach.

The Alliance had created a position of strength and they knew it. Then Atlantis had entered into the picture and had fought against the Wraith without paying any dues to the Alliance Council. After two years of avoiding each other, and the occasional small skirmish, the day had come when the Alliance had agreed to sit down and make a formal non aggression treaty with Atlantis and Earth. Of course that was easier said than done.

John shut the lights of the bathroom off as the door slid open. He paused as he stepped back into the bedroom. The air was surprisingly cold and tasted of late night sea air, but when John looked over to the balcony doors he saw they were closed. Though there was a simple explanation he found himself suddenly cautious. Survival instinct tingled to life and he stepped carefully forward through the half light.

He heard clothing moving behind him and he turned, too late, to find the barrel of an energy weapon aimed at his face. He froze and his eyes darted from the barrel to the finger coiled around the trigger just behind it. The finger didn't move, but it was ready, only a fraction of an inch was all it would take. In the two seconds this took John's mind had already clocked the weapon as being Alliance made, and judging by the extra fins to the sight it looked Genii. Of course that told him nothing, since anyone could get hold of Alliance weapons.

John looked away from the weapon following the arm up to a pair of light blue eyes set among the stark features of a heavily built man. The man seemed familiar somehow, but John couldn't place him yet.

"I think you might have the wrong room," John suggested.

The blue eyes held a glint of amusement and it was pretty clear to John that the man was enjoying this. "No, Sheppard, I have the right room. I want to see your hands up by your head, palms outwards," he ordered.

John did as he was told, and slowly lifted his hands, empty palms facing the intruder. "Who are you?" John demanded, but kept his voice casual, not wishing to show the guy any hint of emotion.

"I am a messenger, that is all you need to know," the intruder replied.

"A note under the door would have been fine," John suggested as he kept his eyes fixed on the man and his steady trigger finger.

"My Master wanted this message delivered personally and in such a manner that it would have your undivided attention."

"Well," John replied as he licked his dry lips, "how about your Master schedules an appointment with me, then we can discuss whatever the issue is…"

The man stepped slightly closer, though not close enough for John to be able to do anything useful. "No, Sheppard, this isn't a discussion and my Master is not expecting a response from you. In fact you will be in no position to answer anyone ever again."

John's heart dropped at that. "Don't you think killing me in Atlantis is a little risky?" John tried a different tactic.

"Life is risk, Sheppard and you have taken your last." John's would be assassin stepped slightly closer, his grip on his weapon shifting and John twitched in response, his body wanting to react, but the assassin was still too far away.

"Do you really think you're going to get away with this?" John demanded, allowing his anger out a little.

The man grinned, showing slightly yellow teeth. "Yes. We have done all our research, Sheppard. No one will know you are dead until tomorrow morning and then it will be too late."

John watched the trigger finger tighten and he knew there wasn't much time left. "Who's your Master then?"

The yellow teeth reappeared, but it was the vague shift of shadows over the assassin's shoulder that caught John's attention, though he kept his gaze on the teeth.

"You will know when you hear the message and then you will have only a single last moment of your life in which to admit defeat to my Master."

A knife slid abrupt over the assassin's shoulder, one edge of the sharp blade touching against the man's throat. John watched the man freeze in response to the touch of cold metal against his carotid artery. The knife pressed a little closer and higher causing the man to tilt his head back. John watched the would-be assassin's weight lift up from his heels in an effort to hold himself away from the blade.

"I don't think you did enough research," John told the man. "Now drop the weapon."

The man thought for a second, but the knife moved a fraction and he loosened his hold on the gun. John reached forward took the weapon quickly, turning it in his hands and saw, as he had suspected, that it was set to kill. John switched it over to stun and held it loosely by his side as he turned to the now pale man.

"So, what was this message then?"

The man looked away, turning his eyes and head as much as he dared, trying to look at the person holding the blade. John stepped forward drawing his attention back to him. "I think you should answer me very quickly; she doesn't like to be kept waiting."

John watched the man's eyes and saw the surprise there; despite all the man's 'research' no one had known about her. It appeared that all their attempts to keep things secret had worked, and in fact it had worked so well that it had literally saved his life tonight. But, it was important that this guy not find out who was holding the Atlantis issue knife to his throat.

John moved closer, using his body and his growing anger to intimidate the man. "Answer me and maybe I'll ask her to spare you."

The man swallowed very carefully and John saw a small drop of blood glisten from the knife's edge. "The message was…that you should aim higher," he man said carefully and John knew instantly who this man's master was.

"Kolya," John muttered with disgust. Kolya had led a small team to take over Atlantis in the first year of the city's occupation during a massive storm that had nearly wiped out the city. Kolya was part of a small group of exiled Genii warriors who had tried to seize power of the Genii government, who were part of the Alliance. Of course that was the official Genii story after John, and those others left in the city when the storm hit, had won out over the Genii invaders. During his escape Kolya had taken Elizabeth hostage and had been using her as a human shield as he made his way to the Gate. John had shot Kolya in the chest, forcing him to release Elizabeth, but Kolya had still escaped through the Gate and it appeared he had survived.

John frowned trying to place the man with the faces he remembered from the Genii. "You're not Genii," John concluded as he looked down at the dark clothes the man wore and pulled open the man's jacket, searching through his pockets until he came up with a small extra energy weapon. John tossed the tiny weapon in his hand and caught it as he looked back at the man. "Your one of Narro's men," he guessed.

The man's eyes narrowed slightly.

"I've seen you with him," John told him as the memories finally clicked. This man had stood beside the Vancet Council member. Vancet was one of the strongest super powers in the Alliance and Narro was one of the most important of their politicians. "You're not Genii."

"I was born on the Genii home world before I was sold to the Vancet," he man replied, his voice full of hatred. It was one of the main sticking points Atlantis had with the Alliance; that most of their number still used slaves. Children, women and men were used as trading commodities across the Alliance, in fact John had personal first hand knowledge of what it was like to be sold as an Alliance slave.

"So, you're a spy for the Genii?" John asked.

"No, I work for Kolya, who will one day rule the Genii," the man protested.

John thought it all through for a few moments. "So you kill me for Kolya and plant this weapon," he showed the small Vancet weapon, "and stop the treaty from being formed. Perhaps even start a war between Atlantis and the Alliance."

The man shut his lips tightly and though the knife bit in closer it was clear he wasn't going to say anymore.

"You got a name?" John asked, but the man closed his eyes and kept his mouth shut. A few more drops of blood appeared on the knife, but John shook his head and the knife dropped away. The man opened his eyes in surprise, but John had lifted the original stunner and blasted him.

The man collapsed down to the floor into an unconscious heap. John turned to a side unit and picked up his radio. "Control, this is Sheppard, I need a security team to my quarters asap. Someone's just tried to kill me."

"They're on their way Major. Do you require a medic as well?" The helpful voice of Chuck asked.

"No, I'm fine and my visitor is just stunned."

"They're on their way and I'll report the incident to Colonel Sumner."

John tried not to sigh at the thought. "No need to wake him up, I'll tell him all about it tomorrow morning." John signed off before Chuck could protest.

John looked up from the crumpled heap of assassin by his boots and turned to the lovely woman who was returning his knife back to its hiding hole under the bed. "You should probably hide," John told her with a wink as he inclined his head towards the bathroom.

She gave him an amused smirk. "I believe you are simply attempting to get back at me for last time," she told him, but she was already moving towards the bathroom door.

John watched her open the door. "No, if I was I would make you hide in the closet."

She gave him an amused glare before the bathroom door closed behind her, which was just in time for the chimes rang announcing the arrival of John's late rescue party. The man was taken away to lock up and John described the entire incident, leaving out his bed mate's part in the story, to Major Lorne. Lorne was clearly appalled that someone should have had the nerve to try this in the city.

"At least they didn't go for Colonel Sumner," John half joked in reply and Lorne gave him a half smirk. Despite the Colonel's clear disapproval of John, John had been accepted by all the rest of the military force, in fact John had made some real good friends in the city. John never openly defied Sumner, but it was well known that there was no love lost between the two.

"Okay, I'll report this first thing to Colonels Carter and Sumner tomorrow morning," Lorne agreed.

"I'll have my report ready in the morning," John replied and with that it was over. Lorne was the last to leave and John locked the doors behind him. He headed over to his bedside table and set down his radio. As he quickly noted down a few thoughts ready for his report tomorrow he heard the bathroom door slide open and then the balcony doors open allowing in the cool night air. Lorne had already looked out there, but John trusted her more than Lorne to find something. John noted down his last notes and set aside his notepad and wandered over to the balcony doors.

It was a cold night, but his body was still rather overheated from his near death experience and the knowledge that Kolya was still alive and out to get him. He stepped out onto the balcony to find her crouched down in one corner, her fingers brushing the ground and then she stood up again. The sea breeze caught her long red hair and danced it around her shoulders. She usually wore it braided back from her face, but she loosened it when they saw each other, knowing he liked to run his fingers through her hair.

"Find something?" He asked softly.

She brushed her hands off and leaned over the corner of the balcony railing, pointing down. John ignored the fact that she would be clearly seen if anyone else was watching his balcony, though in truth where could they be watching from? As John walked to her side he looked up and around to the other balconies some distance away, but there were no obvious points from which to spy on him and there was no balcony on the floors below his. He had chosen this room as his quarters for the space, the view and the balcony. The balcony was set on a corner of the lower levels of the tower, so he had an unobstructed view from his room, which also meant no one could easily spy on him. Of course he now realised it also meant that no one would have been able to see his assassin waiting for him.

John reached her side and leant over the balcony, looking down at where she was pointing.

"He climbed up this way onto the balcony. I saw him enter when you had gone into the bathroom," she told him. John studied the tiny hints that someone had climbed up the wall; the most obvious a partial boot print on a ledge one floor below them.

"Risky," John muttered.

"Indeed," she replied as she stepped back and pointed down to the corner of the balcony. "He waited here." John crouched down as she did and he studied the small amount of dust on the balcony floor. "Where would you find dust this colour in the city?" She asked him as she showed him the light dusting over her fingertips.

John took her hand, bringing the dust and her warmth closer to him. "Maybe out from a pier maybe, but it looks more like soil."

"Perhaps he had just travelled in from off world?" She suggested as she gently pulled her hand from his and brushed the light soil away from her skin.

"Lorne will have checked all that out by morning. I'll take a sample of the soil." He headed back into his quarters to return with a small plastic bag in which his new mp3 player headphones had arrived. He pinched up some of the soil and sealed it up inside the small bag and set in inside beside his notepad. Maybe Rodney's girlfriend, the botanist, could identify where it had come from.

He turned back to the balcony, pausing in the doorway beside her.

"Why would this Kolya wish the treaty to be unsuccessful?" She asked him.

John pulled his gaze up from the sight of her bare legs below the short tailored nightgown she wore. "Umm, he hates Atlantis and me especially. I guess he wants to make things difficult for us."

She turned to him, her arms crossed against the cold sea air. "I have heard talk of dissatisfaction among the Genii."

"Really?" John asked. They had agreed a long time ago to keep politics out of their relationship, but that didn't change the fact that they were from different peoples and that technically some would consider them enemies. She was part of the Alliance military, from the highest sector called the 'Elite'. The Alliance military was a massive and powerful force, which was comprised of peoples from all the worlds within the Alliance. In fact the military had become so successful and unified that its power threatened the Alliance's head Council itself. The opinion and might of the military was a political power of its own right, but one that had never been used openly as a political tool. It was the military and their occasional cooperation with Atlantis that had encouraged this non aggression treaty between the Alliance and Atlantis. It was a dangerous position for the military and the Alliance council and one day that tension would break. John knew that when that day came she would be caught right in the middle of it. He didn't like to think about that.

"We've heard that the supreme leader behaves more like a tyrant, but that's hardly new for the Genii," he said.

She looked out to the sea beyond the balcony, her hair flying out behind her, revealing the long black Wraith tattoos which ran down one side of her throat. Among the Alliance military Elite, anyone who had killed a Wraith Queen in direct hand to hand combat could take part of that Queen's unique tattoo as their own. Some of the most public Elite figures showed off their five or six tattoos openly, but she hid most of hers under her clothing. She was not interested in showing off, though she had to show some to maintain her status. John had personally counted all her tattoos and the final figure was one that he doubted anyone else knew.

"The Genii government is likely to topple, for their leadership has been weakened as they have been tormented by various factions within their own number."

John couldn't hide his surprise at both the news and that she was sharing so much with him. "Any idea how far ahead we're looking till that happens?"

"I do not know, but if they agree to the treaty with your people then their government will look stronger to their people and regain them support."

John looked out at the balcony again, to see that the number of lights shining out from the pier below had finally started to reduce. "I wasn't aware the Genii liked us that much," he asked as he turned back to her.

"They respect your military power and that you are still in control of the city of the Ancestors. They would like to keep a friendship to gain from you."

John nodded, her answer confirming his own opinion of the Genii he had met. "So, I'm thinking Kolya is a main player in this attempt to take control of the Genii government. If the treaty goes ahead, his chances of taking over go down the plughole. So he kills a member of Atlantis and makes it look like the Vancet did it."

"And he gets to take out his personal revenge on you as well," she added. He turned to her to see her dark eyes showing the humour he so enjoyed in her. He glared at her as he moved closer, sliding an arm around her.

"You would miss me if I was gone," he told her as he ran his palm around her hip, tracing out the beautiful curves of her body.

She looked out to the sea, her elegant chin lifted, but there was a touch of a smile she couldn't hide. "I would regret the loss of such a good personal slave."

He narrowed his eyes at her. "I thought we had agreed that episode was behind us," he argued, though he knew she had never considered him her property, as she had freed every slave she had acquired over the years.

She turned her head back towards him, her eyelashes lowered. "In Alliance custom a slave has to be officially freed by their Master or Mistress."

John gave her a smug expression. "So are you saying you can't bear to let me go?"

She laughed lightly, the sound deep and honest. "I would not go that far."

John gave her a hurt look as he resumed stroking her back and hips. "Anyway, you're originally from Athos and they don't believe in keeping slaves, right?"

"My father officially outlawed the keeping and selling of slaves on the Athosian worlds, but that has not stopped some Athosians from using slaves outside of those worlds." She might be arguing the point, but she was turning in his arms, her hands settling against his chest. A burst of satisfaction roared through him, as it did every time she touched him.

"So are you saying you've had other personal slaves before?" John asked as he slid his arms around her, pulling her closer to him. Her hands were pressed against his chest, keeping some distance between them, but he knew she did so only to keep up some resistance in this game they were playing.

"A few," she replied as he ran his hands down to her hips and began to pull up the material of her nightgown until he could slid his hands under it to her soft skin beneath. He watched the soft look of pleasure cross her features as he touched her skin.

"How many?" He asked.

She ran her hands across his chest, her fingers testing his muscle definition and he knew she liked the sensation of his chest hair through his tight soft cotton shirt. He ran his hands up her back, pulling up her nightgown as he went. He could feel the goose bumps rising on her skin as the night air met her bared skin, so he flattened his hands tighter against her back and pulled her closer to his warmth.

She stepped closer as she slid her hands around his sides to his back and her hands moved up under his shirt. "I do not remember," she replied with a smile as she flattened her hands against his back and pulled him towards her.

John leant down to her, drawing in the smell of her, the warmth of her body and the enjoyable prospect of her kiss. But, he paused above her lips and smiled. "Try and remember," he teased.

He saw her glare and that she rolled her eyes, but he had her nightgown up to her shoulders and he drew his hands round to her sides, grazing his fingers against the outer edges of her breasts. He felt her shiver slightly and knew that this time it had nothing to do with the sea air through the open balcony doors. With a thought the balcony doors slid shut abruptly and the room was suddenly warmer and more intimate.

She smiled now, her hands moving against his back, her fingers caressing and distracting him. "You are the first I have decided to keep," she replied with a deep whispered voice.

She pulled back from him, pulling out of his arms and he let her, and her nightgown, go. He knew she was teasing him with her comment, but he couldn't let it go. She moved away lifting up her nightgown, pulling it up over her head. Her glorious back, with its diagonal line of twisting beautiful tattoos across it, was highlighted in the pale light as she walked away towards the bed. "I'm not a slave," John told her, though his voice sounded more like a devoted follower than ever before.

She reached his bed and turned back to him, standing proud and tall in her nakedness. The lines of tattoos snaked down from her throat, down one side of her cleavage, disappearing round one side of her ribcage, to reappear at her other hip to run past her belly to one shapely thigh. She tilted her head and smiled at him.

"Neither am I," she replied and turned back to the bed.

John pulled his shirt up and off as he followed her. He reached her as she climbed onto the bed in which they had already enjoyed each other earlier that night. He pulled off his boxers as he climbed after her, pulling her to him and under him as he encouraged her down to the mattress. She smiled as she reached up and pulled him down tightly against her till their lips met. He returned her passionate kiss and devoted the rest of the night to worshipping his Mistress.

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END


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